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3D electron diffraction structure of Hen Egg-White Lysozyme from nano-crystals obtained by high pressure freezing and cryo-sectioning
ELECTRON CRYSTALLOGRAPHY
Crystal Data
Unit Cell
Length ( Å )
Angle ( ˚ )
a = 76.887
α = 90
b = 76.887
β = 90
c = 37.761
γ = 90
Symmetry
Space Group
P 43 21 2
Refinement
Statistics
Diffraction ID
Structure Solution Method
Cross Validation method
Resolution (High)
Resolution (Low)
Number Reflections (Observed)
Number Reflections (R-Free)
Percent Reflections (Observed)
R-Factor (All)
R-Work (Depositor)
R-Work (DCC)
R-Free (Depositor)
R-Free (DCC)
Mean Isotropic B
ELECTRON CRYSTALLOGRAPHY
FREE R-VALUE
2.91
54.367
2638
276
96.418
0.214
0.2048
0.2048
0.2949
0.2957
31.961
Temperature Factor Modeling
Anisotropic B[1][1]
Anisotropic B[1][2]
Anisotropic B[1][3]
Anisotropic B[2][2]
Anisotropic B[2][3]
Anisotropic B[3][3]
-0.063
-0.063
0.125
RMS Deviations
Key
Refinement Restraint Deviation
r_dihedral_angle_2_deg
32.428
r_dihedral_angle_3_deg
21.077
r_dihedral_angle_4_deg
17.784
r_dihedral_angle_1_deg
8.368
r_lrange_it
6.524
r_lrange_other
6.521
r_mcangle_other
3.819
r_mcangle_it
3.797
r_scangle_it
3.41
r_scangle_other
3.409
RMS Deviations
Key
Refinement Restraint Deviation
r_dihedral_angle_2_deg
32.428
r_dihedral_angle_3_deg
21.077
r_dihedral_angle_4_deg
17.784
r_dihedral_angle_1_deg
8.368
r_lrange_it
6.524
r_lrange_other
6.521
r_mcangle_other
3.819
r_mcangle_it
3.797
r_scangle_it
3.41
r_scangle_other
3.409
r_mcbond_it
2.165
r_mcbond_other
2.102
r_scbond_it
1.897
r_scbond_other
1.875
r_angle_refined_deg
1.489
r_angle_other_deg
1.205
r_nbd_refined
0.225
r_symmetry_nbd_other
0.188
r_nbtor_refined
0.169
r_nbd_other
0.16
r_xyhbond_nbd_refined
0.158
r_symmetry_nbd_refined
0.117
r_symmetry_nbtor_other
0.078
r_chiral_restr
0.059
r_bond_refined_d
0.005
r_gen_planes_refined
0.005
r_bond_other_d
0.001
r_gen_planes_other
0.001
Software
Software
Software Name
Purpose
REFMAC
refinement
Sample
Monomer of Hen Egg-White Lysozyme
Specimen Preparation
Sample Aggregation State
3D ARRAY
Vitrification Instrument
Cryogen Name
NITROGEN
Sample Vitrification Details
Freezing carried out at high pressure (210 MPa) and -196 C, using a Leica EM HPM100
Staining Type
NONE
Staining Material
Brilliant blue
Staining Details
The blue dye (Brillant blue) is used to see the crystals during cryo-sectioning
Embedding Material
dextran
Embedding Details
40% Dextran in phosphate buffer
3D Reconstruction
Reconstruction Method
CRYSTALLOGRAPHY
Number of Particles
Reported Resolution (Å)
2.91
Resolution Method
DIFFRACTION PATTERN/LAYERLINES
Other Details
Diffraction data were processed with XDS and merged with XSCALE. The structure was solved by molecular replacement with PHASER 2.8.3 and refined with ...
Diffraction data were processed with XDS and merged with XSCALE. The structure was solved by molecular replacement with PHASER 2.8.3 and refined with Refmac 5.8.0267, using electron atomic scattering factors (source electron used in Refmac).
Refinement Type
Symmetry Type
3D CRYSTAL
Space Group Name
Length a
76.89
Length b
76.89
Length c
76.89
Angle Alpha
90
Angle Beta
90
Angle Gamma
90
Map-Model Fitting and Refinement
Id
1
Refinement Space
Refinement Protocol
OTHER
Refinement Target
Overall B Value
Fitting Procedure
Details
Data Acquisition
Detector Type
OTHER
Electron Dose (electrons/Å**2)
0.004
Imaging Experiment
1
Date of Experiment
Temperature (Kelvin)
Microscope Model
FEI TECNAI F20
Minimum Defocus (nm)
Maximum Defocus (nm)
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS
Imaging Mode
DIFFRACTION
Specimen Holder Model
GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER
Nominal Magnification
Calibrated Magnification
Source
FIELD EMISSION GUN
Acceleration Voltage (kV)
200
Imaging Details
Camera length used 730 mm and 1000 mm (corresponding to 1285 and 1825 mm calibrated values)